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High-throughput sequencing makes it possible to study epigenetic properties such as DNA methylation genome-wide with single base pair precision. Two research projects were done studying epigenetic properties in plants using high-throughput sequencing using DNA from the model organism Arabidopsis Thaliana. The first project looks at the conservation of DNA methylation on an evolutionary time scale to determine to what degree DNA methylation is conserved with respect to the underlying DNA sequence. This is done by comparing pairs of duplicated genes in Arabidopsis resulting from a genome duplication event 40-80 million years ago in addition to non-coding repeats in the genome. DNA methylation was found to be significantly conserved but methylated cytosines had a tendency to deaminate to thymine which was the most common type of mutation in the underlying DNA sequence. In the second project DNA methylation, nucleosome density and gene expression are compared between tissues in Arabidopsis. Using shoots (entire above ground section) and roots as two different tissues, significant epigenetic differences are found in certain genes, related in function, between the two tissue types. Methylation and nucleosome density are found to be periodic in nature and similar between shoot and root at a genome-wide scale. Positioning of methylation and nucleosomes across the gene body show significant change among genes that are differentially expressed between shoot and root.

Numerous clinical conditions continue to drive the need to understand, both quantitatively and mechanistically, the relationship between physical forces and bone formation and adaptation. The global objective of this research was to investigate the influence of strain environment on patterns of tissue differentiation. To test hypotheses related to this overall objective, animal models of distraction osteogenesis (DO) were implemented to study how physical forces and strains influence bone regeneration at different stages of the repair process. The approach taken was: (1) to manipulate the mechanical environment within the mesenchymal gap tissue in vivo in a known fashion; (2) to predict the resulting changes in stresses and strains by computational and analytic means; and (3) to assess the effects of these changes on patterns of tissue differentiation. Correlations between strain environment and tissue response were then sought to gain insight into the relationship between these two entities. Both the time-dependent and large-deformation behavior of the mesenchymal distraction gap tissue were evaluated. The strain environment was then manipulated in three specific ways, and the effects of these changes on patterns of new bone formation and precursor tissue differentiation were assessed. Gap tissue was shown to be viscoelastic and did not relax completely after each distraction, leading to tension accumulation during repeated elongations. The ability of a finite element/optimization scheme to accurately predict experimental load-displacement curves gave us confidence in our predictions of strain environment within the gap tissue, critical for the testing of our hypotheses. Specific correlations between tissue-level strains and patterns of tissue response were observed. Eight-fold reductions in strain magnitude appeared to induce significant changes in trabecular architecture. Temporal patterns of bone and cartilage differentiation depended significantly on rate of distraction. These findings, coupled with the predicted stress accumulation from viscoelasticity analyses, implicate a damage mechanism for these changes. Altered distortional strains effected marked changes in new bone volume and precursor tissue proliferation. The results of these studies provide direct evidence that tissues are sensitive to the local strain environment through any of several mechanisms including blood supply, stem cell availability, and scaffolding architecture.